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Selected R packages

Metagenomics

Phylogeny

Visualization

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Last updated on 2021-12-23.

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Shuangbin Xu

A Ph.D. student of Bioinformatics, I am broadly interested in metagenomics, bioinformatics, machine learning, data mining and visualization.

I have leaded and contributed to developing some R packages, including MicrobiotaProcess, ggtreeExtra, ggstar, ggbreak, ggtree, treeio, tidytree and ggmsa, to help related researchers to explore and understand their data.

Education

Ph.D., Bioinformaitcs

Southern Medical University

ChuangZhou, CN

current - 2019

  • Thesis: The development of computational methods for studying microbiome: focus on the data mining and visualization

M.S.,Aquatic Biology

JiMei University

Xiamen, CN

2017 - 2014

  • Thesis: 大黄鱼环状RNA挖掘与功能分析

B.S., Aquaculture

Northwest A&F University

XianYang, CN

2014 - 2010

Work Experience

Senior Bioinformatics Engineer

Xiamen TreatGut Company

XiaMen, CN

2019 - 2017

  • Helping build the workflow of microbiome data analysis
  • Helping the mining of related microbiome data
  • Helping develop the related testing products

Bioinformatics Engineer Intern

Frasergen Genetic Information Company

Wuhan, CN

2016

  • Helping the deployment and using with slurm and pbs scheduling systems of the software (PacBio diploid assembler: Falcon, canu, etc) of the TianHe and company’s Supercomputer platform

Publications

  • Citation = 317
  • H-index = 8
  • I10-index = 7

First (and co-first) Author

ggtreeExtra: Compact visualization of richly annotated phylogenetic data

Molecular Biology and Evolution. 2021, 38(9):4039-4042.

N/A

2021

  • S Xu, Z Dai, P Guo,X Fu, S Liu, L Zhou, W Tang, T Feng, M Chen, L Zhan, T Wu, E Hu, Y Jiang*, X Bo*, G Yu*
  • Impact Factor2020 = 16.24

Use ggbreak to effectively utilize plotting space to deal with large datasets and outliers

Frontiers in Genetics. 2021, 12:774846.

N/A

  • S Xu#, M Chen#, T Feng, L Zhan, L Zhou, G Yu*
  • Impact Factor2020 = 4.599

Gut microbiota and metabolite alterations associated with reduced bone mineral density or bone metabolic indexes in postmenopausal osteoporosis

Aging (Albany NY). 2020, 12(9):8583-8604.

N/A

2020

  • J He#, S Xu#, B Zhang#, C Xiao, Z Chen, F Si, J Fu, X Lin, G Zheng*, G Yu*, J Chen*
  • Impact Factor2020 = 5.682

Leveraging Fecal Bacterial Survey Data to Predict Colorectal Tumors

Frontiers in Genetics. 2019, 10:447.

N/A

2019

  • B Zhang#,S Xu#, W Xu#, Q Chen, Z Chen, C Yan, Y Fan, H Zhang, Q Liu, J Yang, J Yang, C Xiao, H Xu*, J Ren*
  • Impact Factor2019 = 3.258

Transcriptome-wide identification and functional investigation of circular RNA in the teleost large yellow croaker (Larimichthys crocea)

Marine genomics. 2017, 32:71-78

N/A

2017

  • S Xu, S Xiao, C Qiu, Z Wang*
  • Impact Factor2017 = 1.937

Contributing Author

clusterProfiler 4.0: A universal enrichment tool for interpreting omics data

The Innovation. 2021, 2(3):100141.

N/A

2021

  • T Wu#, E Hu#, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo*, G Yu*

treeio: an R package for phylogenetic tree input and output with richly annotated and associated data

Molecular Biology and Evolution. 2020, 37(2):599-603.

N/A

2020

  • LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu*
  • Impact Factor2020 = 16.24

Preservation of the fecal samples at ambient temperature for microbiota analysis with a cost-effective and reliable stabilizer EffcGut

Science of The Total Environment. 2020, 741:140423.

N/A

  • L Yang#, K Hou#, B Zhang#, C Ouyang, A Lin, S Xu, D Ke, L Fang, Q Chen, J Wu, C Yan, Y Lian, T Jiang, J He, H Wang, Y Fu, C Xiao, Z Chen*
  • Impact Factor2020 = 7.963

Genome-wide association study using single marker analysis and Bayesian methods for the gonadosomatic index in the large yellow croaker

Aquaculture. 2018, 486:26-30.

N/A

2018

  • Y Gao#, L Dong#, S Xu, S Xiao, M Fang, Z Wang*
  • Impact Factor2018 = 3.022

Cloning and expression profiling of gsdf and amh genes in large yellow croaker (Larimichthys crocea)

South China Fisheries Science. 2017, 13(6):1-13.

N/A

2017

  • A Lin, Y Xie, S Xu, K Ye, S Gong, Z Wang*

Identification of a male-specific DNA marker in the large yellow croaker (Larimichthys crocea)

Aquaculture. 2017, 480:116-122.

N/A

  • A Lin, S Xiao, S Xu, K Ye, X Lin, S Sun, Z Wang*
  • Impact Factor2017 = 2.71

Rapid construction of genome map for large yellow croaker (Larimichthys crocea) by the whole-genome mapping in BioNano Genomics Irys system

BMC Genomics. 2015, 16(1):1-10

N/A

2015

  • S Xiao, J Li, F Ma, L Fang, S Xu, W Chen, Y Wang*
  • Impact Factor2015 = 3.867

Conference proceedings

Analysis and visualization of microbiome datasets using MicrobiotaProcess

The 10th BiocAsia2020 Conference, 2020

Virtual Conference

2020